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July 7, 2019

The ‘gifted’ actinomycete Streptomyces leeuwenhoekii.

Streptomyces leeuwenhoekii strains C34T, C38, C58 and C79 were isolated from a soil sample collected from the Chaxa Lagoon, located in the Salar de Atacama in northern Chile. These streptomycetes produce a variety of new specialised metabolites with antibiotic, anti-cancer and anti-inflammatory activities. Moreover, genome mining performed on two of these strains has revealed the presence of biosynthetic gene clusters with the potential to produce new specialised metabolites. This review focusses on this new clade of Streptomyces strains, summarises the literature and presents new information on strain C34T.

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July 7, 2019

Natural rubber and the Russian dandelion genome

The world needs rubber. Rubber is crucial for the tires on the cars, trucks and airplanes that propel modern transportation. It is equally important for daily tasks: latex gloves in the lab, balloons in angioplasty and wetsuits that warm a cold dip in the ocean. Rubber can be made synthetically from petroleum derivatives, but synthetic rubber is not as strong as rubber iso- lated from plants. The principal plant source for natural rubber (NR) is the sap of the Par´ a tree (Hevea brasiliensis), which is grown throughout Southeast Asia. Unfortunately, the produc- tion capacity of the Par´ a tree is limited by the availability of suitable land and by labor-intensive harvesting methods. The sustainability of the Par´ a crop is also constrained by its narrow genetic base, which may make the crop susceptible to disease.

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July 7, 2019

Complete genome sequence of a heavy metal resistant bacterium Maribacter cobaltidurans B1T, isolated from the deep-sea sediment of the South Atlantic Ocean

Many bacteria in the environment have adopted to the presence of toxic heavy metals. Here we present the complete genome sequence of a heavy metal resistant bacterium, Maribacter cobaltidurans B1T (=CGMCC 1.15508T=KCTC 52882T=MCCC 1K03318T), which was isolated from a deep-sea sediment sample collected from the South Atlantic Ocean. Strain B1T is able to resist high concentrations of Co2+ (10.0mM) in Marine Agar 2216. The genome of strain B1T comprises 4,639,957bp in a circular chromosome with G+C content of 39.7mol%. Resistance to Co2+ is mainly based on efflux system in the genome of stain B1T, including czcCBA operons, czcD genes, corC genes, etc. Comparing with the closely related species M. orientalis DSM 16471T, the genome of B1T harbors twenty more copies of genes in czcCBA operon and two copies of the czcD genes related to Co2+ efflux. The function of these genes may contribute to the high level of cobalt resistance, revealing its potential application in biotechnological industry.

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July 7, 2019

The complete genome sequence of Colwellia sp. NB097-1 reveals evidence for the potential genetic basis for its adaptation to cold environment

Colwellia sp. NB097-1, isolated from a marine sediment sample from the Bering Sea, is a psychrophilic bacterium whose optimal and maximal growth temperatures were 13 and 25°C, respectively. Here, we present the complete genome of Colwellia sp. NB097-1, which was 4,661,274bp in length with a GC content of 38.5%. The genome provided evidence for the potential genetic basis for its adaptation to a cold environment, such as producing compatible solutes and cold-shock proteins, increasing membrane fluidity and synthesizing glycogen. Some cold-adaptive proteases were also detected in the genome of Colwellia sp. NB097-1. Protease activity analysis further showed that extracellular proteases of Colwellia sp. NB097-1 remained active at low temperatures. The complete genome sequence may be helpful to reveal how this strain survives at low temperature and to find cold-adaptive proteases that may be useful to industry.

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July 7, 2019

Complete genome of Halomonas aestuarii Hb3, isolated from tidal flat

Halomonas aestuarii Hb3, a moderately halophilic bacterium belonging to the class Gammaproteobacteria, was isolated from a tidal flat. Herein, we report the complete genome sequence of its strain Hb3. Its size is estimated at 3.54Mbp with a mean G+C content of 67.9%. The genome includes 3238 open reading frames, 65 transfer RNAs, and four ribosomal RNA gene operons. Genes related to the degradation of monoaromatic compounds, detoxification of arsenic, and production of polymers were identified. These features indicate that this strain may be important for ecological and industrial application.

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July 7, 2019

Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a flavobacterium isolated from coastal surface seawater

Here we present the complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a flavobacterium isolated from coastal surface seawater. A 3.3Mb genome revealed remarkable specialization of this bacterium particularly in the degradation of sulfated polysaccharides available as detritus or in dissolved phase. Besides utilizing high molecular weight organic biopolymers, this strain appears to accomplish assimilatory sulfate reduction, sulfide oxidation, and acquisition and inter-conversion of inorganic carbon. Genes encoding zeaxanthin and three different kinds of DNA photolyase/cryptochrome (senses blue light) were present, while genes that code for blue light sensing BLUF domain proteins and red/far-red light sensing phytochromes were absent. Furthermore, CC-SAMT-1T lacked the rhodopsin photosystem and all other genes that confer any other known forms of phototrophy. The genomic data revealed that CC-SAMT-1T is highly adapted to sulfur-rich coastal environments, where it most likely contributes to marine carbon and sulfur cycles by metabolizing sulfated polysaccharides as well as inorganic sulfur.

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July 7, 2019

Complete genomes of the marine flavobacterium Nonlabens strains YIK11 and MIC269

Here, we report the complete genome sequences of two strains, which were isolated from sediment samples collected in Korea and Micronesia, and both were classified as members of Nonlabens spp. The complete genome sequence of Nonlabens sp. strain YIK11 consists of 3,260,677bp in two contigs while the one from strain MIC269 consists of 2,884,293bp in one contig, without plasmid. The genomes of YIK11 and MIC269 contain three and two genes encoding rhodopsins of different types, respectively.

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July 7, 2019

Genome sequencing to develop Paenibacillus donghaensis strain JH8T (KCTC 13049T=LMG 23780T) as a microbial fertilizer and correlation to its plant growth-promoting phenotype

Paenibacillus donghaensis JH8T (KCTC 13049T=LMG 23780T) is a Gram-positive, mesophilic, endospore-forming bacterium isolated from East Sea sediment at depth of 500m in Korea. The strain exhibited plant cell wall hydrolytic and plant growth promoting abilities. The complete genome of P. donghaensis strain JH8T contains 7602 protein-coding sequences and an average GC content of 49.7% in its chromosome (8.54Mbp). Genes encoding proteins related to the degradation of plant cell wall, nitrogen-fixation, phosphate solubilization, and synthesis of siderophore were existed in the P. donghaensis strain JH8T genome, indicating that this strain can be used as an eco-friendly microbial agent for increasing agricultural productivity.

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July 7, 2019

Complete genome sequence of Granulosicoccus antarcticus type strain IMCC3135T, a marine gammaproteobacterium with a putative dimethylsulfoniopropionate demethylase gene

Granulosicoccus, the only genus of the family Granulosicoccaceae, occupies a distinct phylogenetic position within the order Chromatiales of the Gammaproteobacteria. The genus has been found in various marine regions, especially associated with diverse marine macroalgae. No genomes have been reported for the genus Granulosicoccus thus far, hampering studies on physiology and lifestyles of this genus. Here we report the complete genome sequence of strain IMCC3135T, the type strain of Granulosicoccus antarcticus isolated from Antarctic coastal seawater. The genome was 7.78Mbp long and harbored many genes involved in sulfur metabolism. In particular, a gene for dimethylsulfoniopropionate (DMSP) demethylase was found in the genome, rendering strain IMCC3135T one of the few marine gammaproteobacteria equipped with the potential for DMSP demethylation.

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July 7, 2019

Complete genome sequence of the halophile bacterium Kushneria marisflavi KCCM 80003T, isolated from seawater in Korea

We present the genome sequence of Kushneria marisflavi KCCM 80003T isolated from Yellow Sea in Korea. The complete genome of KCCM 80003T consisted of a single, circular chromosome of 3,667,185bp, with an average G+C content of 59.05%, and 3287 coding sequences, 12 rRNAs, and 66 tRNAs. Kushneria marisflavi KCCM 80003T, belonging to the family Halomonadaceae, exhibited resistance to high salt concentrations and possessed potassium metabolism- or osmotic stress-related coding sequences, including potassium homeostasis, ectoine biosynthesis and regulation, choline and betaine uptake, and betaine biosynthesis features in the genome. These results provide a basis for understanding resistance strategies to osmotic stress at the genetic level and accordingly have implications for genetic engineering and biotechnology.

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July 7, 2019

Complete genome sequence of Tsukamurella sp. MH1: A wide-chain length alkane-degrading actinomycete.

Tsukamurella sp. strain MH1, capable to use a wide range of n-alkanes as the only carbon source, was isolated from petroleum-contaminated soil (Pite?ti, Romania) and its complete genome was sequenced. The 4,922,396?bp genome contains only one circular chromosome with a G?+?C content of 71.12%, much higher than the type strains of this genus (68.4%). Based on the 16S rRNA genes sequence similarity, strain MH1 was taxonomically identified as Tsukamurella carboxydivorans. Genome analyses revealed that strain MH1 is harboring only one gene encoding for the alkB-like hydroxylase, arranged in a complete alkane monooxygenase operon. This is the first complete genome of the specie T. carboxydivorans, which will provide insights into the potential of Tsukamurella sp. MH1 and related strains for bioremediation of petroleum hydrocarbons-contaminated sites and into the environmental role of these bacteria. Copyright © 2017. Published by Elsevier B.V.

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July 7, 2019

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile

Rhodococcus sp. H-CA8f was isolated from marine sediments obtained from the Comau fjord, located in Northern Chilean Patagonia. Whole-genome sequencing was achieved using PacBio RS II platform, comprising one closed, complete chromosome of 6,19?Mbp with a 62.45% G?+?C content. The chromosome harbours several metabolic pathways providing a wide catabolic potential, where the upper biphenyl route is described. Also, Rhodococcus sp. H-CA8f bears one linear mega-plasmid of 301?Kbp and 62.34% of G?+?C content, where genomic analyses demonstrated that it is constituted mostly by putative ORFs with unknown functions, representing a novel genetic feature. These genetic characteristics provide relevant insights regarding Chilean marine actinobacterial strains.

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July 7, 2019

Synthetic biology, genome mining, and combinatorial biosynthesis of NRPS-derived antibiotics: a perspective.

Combinatorial biosynthesis of novel secondary metabolites derived from nonribosomal peptide synthetases (NRPSs) has been in slow development for about a quarter of a century. Progress has been hampered by the complexity of the giant multimodular multienzymes. More recently, advances have been made on understanding the chemical and structural biology of these complex megaenzymes, and on learning the design rules for engineering functional hybrid enzymes. In this perspective, I address what has been learned about successful engineering of complex lipopeptides related to daptomycin, and discuss how synthetic biology and microbial genome mining can converge to broaden the scope and enhance the speed and robustness of combinatorial biosynthesis of NRPS-derived natural products for drug discovery.

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July 7, 2019

Complete genome sequence of the poly-?-glutamate-synthesizing Bacterium Bacillus subtilis Bs-115.

Bacillus subtilis Bs-115 was isolated from the soil of a corn field in Yutai County, Jinan City, Shandong Province, People’s Republic of China, and is characterized by the efficient synthesis of poly-?-glutamate (?-PGA), with corn saccharification liquid as the sole energy and carbon source during the process of ?-PGA formation. Here, we report the complete genome sequence of Bacillus subtilis Bs-115 and the genes associated with poly-?-glutamate synthesis. Copyright © 2018 Wang et al.

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